Heart rate variability (HRV), a cardiac vagal tone indicator, has been proven to predict performance on some cognitive tasks that rely on the prefrontal cortex. However, the relationship between vagal tone and working memory remains understudied. This study explores the link between vagal tone and working memory function, combined with behavioral tasks and functional near-infrared spectroscopy (fNIRS). A total of 42 undergraduate students were tested for 5-min resting-state HRV to obtain the root mean square of successive differences (rMSSD) data, and then divided into high and low vagal tone groups according to the median of rMSSD data. The two groups underwent the n-back test, and fNIRS was used to measure the neural activity in the test state. ANOVA and the independent sample t-test were performed to compare group mean differences, and the Pearson correlation coefficient was used for correlation analysis. The high vagal tone group had a shorter reaction time, higher accuracy, lower inverse efficiency score, and lower oxy-Hb concentration in the bilateral prefrontal cortex in the working memory tasks state. Furthermore, there were associations between behavioral performance, oxy-Hb concentration, and resting-state rMSSD. Our findings suggest that high vagally mediated resting-state HRV is associated with working memory performance. High vagal tone means a higher efficiency of neural resources, beneficial to presenting a better working memory function.